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- PDB-6twq: MAGI1_2 complexed with a 16E6 peptide -

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Basic information

Entry
Database: PDB / ID: 6twq
TitleMAGI1_2 complexed with a 16E6 peptide
Components
  • Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
  • THR-ARG-ARG-GLU-THR-GLN-LEU
KeywordsPEPTIDE BINDING PROTEIN / phosphorylation / motif / PDZ domain
Function / homology
Function and homology information


positive regulation of low-density lipoprotein particle receptor binding / symbiont-mediated suppression of host transcription / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process ...positive regulation of low-density lipoprotein particle receptor binding / symbiont-mediated suppression of host transcription / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / regulation of proteolysis / calcium-dependent phospholipid binding / negative regulation of receptor internalization / activation of GTPase activity / collagen fibril organization / Dissolution of Fibrin Clot / S100 protein binding / virion binding / positive regulation of low-density lipoprotein receptor activity / osteoclast development / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / bicellular tight junction / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / cell-matrix adhesion / response to activity / PDZ domain binding / adherens junction / lung development / calcium channel activity / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / cell junction / late endosome membrane / midbody / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / basolateral plasma membrane / symbiont-mediated perturbation of host ubiquitin-like protein modification / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / host cell cytoplasm / molecular adaptor activity / early endosome / endosome / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / lysosomal membrane / virus-mediated perturbation of host defense response / DNA-templated transcription / calcium ion binding / host cell nucleus / Neutrophil degranulation / nucleolus / cell surface / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 / Annexin A2 / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats ...Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 / Annexin A2 / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CITRIC ACID / Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1 / Protein E6 / Annexin A2
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGogl, G. / Cousido-Siah, A. / Trave, G.
CitationJournal: Structure / Year: 2020
Title: Dual Specificity PDZ- and 14-3-3-Binding Motifs: A Structural and Interactomics Study.
Authors: Gogl, G. / Jane, P. / Caillet-Saguy, C. / Kostmann, C. / Bich, G. / Cousido-Siah, A. / Nyitray, L. / Vincentelli, R. / Wolff, N. / Nomine, Y. / Sluchanko, N.N. / Trave, G.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
C: THR-ARG-ARG-GLU-THR-GLN-LEU
D: THR-ARG-ARG-GLU-THR-GLN-LEU
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,87420
Polymers98,6724
Non-polymers1,20116
Water1,06359
1
B: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
C: THR-ARG-ARG-GLU-THR-GLN-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,05311
Polymers49,3362
Non-polymers7179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-55 kcal/mol
Surface area21500 Å2
MethodPISA
2
D: THR-ARG-ARG-GLU-THR-GLN-LEU
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8219
Polymers49,3362
Non-polymers4857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-38 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.810, 97.130, 201.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 4 molecules BACD

#1: Protein Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / ...Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36


Mass: 48099.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAGI1, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: H7C535, UniProt: P07355
#2: Protein/peptide THR-ARG-ARG-GLU-THR-GLN-LEU


Mass: 1236.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus type 16 / References: UniProt: P03126*PLUS

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Non-polymers , 4 types, 75 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 22% PEG3000, 100 mM Na-citrate (pH 5.5), 100 mM Na-citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→48.58 Å / Num. obs: 35247 / % possible obs: 99.2 % / Redundancy: 13.5 % / Biso Wilson estimate: 70.16 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.45
Reflection shellResolution: 2.65→2.72 Å / Mean I/σ(I) obs: 1.39 / Num. unique obs: 2554 / CC1/2: 0.735

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N7D

5n7d


Resolution: 2.65→48.56 Å / SU ML: 0.4101 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.2181
RfactorNum. reflection% reflection
Rfree0.2621 1739 4.94 %
Rwork0.2388 --
obs0.2399 35168 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 87.87 Å2
Refinement stepCycle: LAST / Resolution: 2.65→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6762 0 62 59 6883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286907
X-RAY DIFFRACTIONf_angle_d0.5369293
X-RAY DIFFRACTIONf_chiral_restr0.03781034
X-RAY DIFFRACTIONf_plane_restr0.00361203
X-RAY DIFFRACTIONf_dihedral_angle_d24.82012640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.730.36971310.37752759X-RAY DIFFRACTION99.86
2.73-2.820.40461540.36722658X-RAY DIFFRACTION98.05
2.82-2.920.36691460.33082733X-RAY DIFFRACTION98.39
2.92-3.030.3531530.31952759X-RAY DIFFRACTION99.22
3.03-3.170.29761440.30872758X-RAY DIFFRACTION99.62
3.17-3.340.35291570.29312734X-RAY DIFFRACTION98.97
3.34-3.550.28621510.27342763X-RAY DIFFRACTION99.22
3.55-3.820.26541540.24952763X-RAY DIFFRACTION98.95
3.82-4.210.26381280.22292814X-RAY DIFFRACTION99.63
4.21-4.810.21171230.19922829X-RAY DIFFRACTION99.43
4.81-6.060.2261510.22182874X-RAY DIFFRACTION99.67
6.06-48.560.20941470.1862985X-RAY DIFFRACTION99.15
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.96505513762-0.0425416487482-2.304767470570.175892798216-0.4551617317450.6047768039810.0638955409794-0.318047084921-0.01580308679320.104583729027-0.2242499243420.008214852035530.09397616130880.3837099798570.1626371816520.741933852921-0.147671795450.02751538656921.20028847216-0.1025683768910.577566329786-46.997795444410.0677938852-7.509504722
23.03188350702-0.3058449865351.497614532321.232337629550.004429965044682.2983437035-0.374991094376-0.3220974295530.519538549910.04002684180360.017805613933-0.0406693984967-0.6796832257660.05156729543570.2659298606310.592614263854-0.160995849288-0.0693765436510.49617940189-0.08113471695740.556935082951-34.791162715322.1863985533-34.7939603446
30.7451498031770.403407254282-0.5576378342390.905450885238-0.9607356645061.038259978210.1298255632010.1928350748350.090727706493-0.4673029077790.205511096862-0.210148502026-0.09965230090930.16005367961-0.3654476952951.16461967658-0.008833706729390.2107308291911.16682171431-0.006983016055750.818928720755-62.141762864718.2904653454-15.4063594334
40.00262121873779-0.0112576210405-0.0100912013786-0.001772256260980.008411076033440.000571990239034-0.07306004113610.06299145613290.121254949754-0.1254612768130.01835192660980.1123596725650.0808719428609-0.1887305449770.01428056333521.50065649649-0.227374132394-0.2248011209481.98620542288-0.3460875850152.01742140529-35.542989186659.9165492168-22.5656028367
50.763952883083-0.0241266888798-0.000680394356168-0.333195189018-0.245722997038-0.335584091870.00997456589992-0.0796930301361-0.0227516863242-0.001999637399550.432181468017-0.4307436678310.446524074740.538019579576-0.3817104840991.37485885954-0.120874609436-0.1329488289251.70373427873-0.2709283932781.20664715236-31.501302867670.322208239-24.16600816
61.67633837232-0.840211730976-0.3663101969471.03822204440.4944586888194.2882024057-0.102632546455-0.154542611225-0.02612719055340.1163835025970.03375326910810.0537027214885-0.278807820922-0.01567068376430.07246007522450.3927586693940.0200931392758-0.06881107766350.315782195351-0.005855207774340.508727300917-57.854103846657.4160089139-36.4993006374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 457 through 644 )
2X-RAY DIFFRACTION2chain 'B' and (resid 645 through 878 )
3X-RAY DIFFRACTION3chain 'C' and (resid 152 through 158 )
4X-RAY DIFFRACTION4chain 'D' and (resid 152 through 158 )
5X-RAY DIFFRACTION5chain 'A' and (resid 458 through 573 )
6X-RAY DIFFRACTION6chain 'A' and (resid 574 through 878 )

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